Classify: (Re)classify after running 'CHETAHclassifier' using a...

Description Usage Arguments Value Examples

View source: R/Utils_CHETAH.R

Description

(Re)classify after running CHETAHclassifier using a confidence threshold
NOTE: In case of bulk reference profiles: only the correlations will be used, as the data does not allow for profile or confidence scores to be calculated.

Usage

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Classify(input, thresh = 0.1, return_clas = FALSE)

Arguments

input

a SingleCellExperiment on which CHETAHclassifier has been run

thresh

a confidence threshold between -0 and 2.
Selecting 0 will classify all cells, whereas 2 will result i n (almost) no cells to be classified.
recommended: between 0.1 (fairly confident) and 1 (very confident)

return_clas

Instead of returning the SingleCellExperiment, only return the classification vector

Value

a charachter vector of the cell types with the names of the cells

Examples

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## Classify all cells
input_mel <- Classify(input_mel, 0)

## Classify only cells with a very high confidence
input_mel <- Classify(input_mel, 1)

## Back to the default
input_mel <- Classify(input_mel)

## Return only the classification vector
input_mel <- Classify(input_mel, 1, return_clas = TRUE)

CHETAH documentation built on Nov. 8, 2020, 8:02 p.m.